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Magnesium in PDB 7o63: High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf)

Enzymatic activity of High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf)

All present enzymatic activity of High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf):
1.16.3.1;

Protein crystallography data

The structure of High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf), PDB code: 7o63 was solved by C.Pozzi, S.Ciambellotti, G.Tassone, P.Turano, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.10 / 1.16
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.133, 184.133, 184.133, 90, 90, 90
R / Rfree (%) 12.5 / 14

Other elements in 7o63:

The structure of High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf) also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf) (pdb code 7o63). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf), PDB code: 7o63:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in 7o63

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Magnesium binding site 1 out of 13 in the High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:12.9
occ:0.90
 OE2 A:GLU27 1.9 12.8 1.0
O A:HOH379 1.9 21.2 1.0
OE1 A:GLU62 2.0 13.0 1.0
O A:HOH340 2.1 16.5 1.0
ND1 A:HIS65 2.2 13.0 0.9
O A:HOH318 2.3 16.9 0.3
ND1 A:HIS65 2.4 12.2 0.1
CD A:GLU27 3.0 12.3 1.0
CD A:GLU62 3.0 12.5 1.0
CE1 A:HIS65 3.1 13.6 0.9
CG A:HIS65 3.3 12.4 0.9
CE1 A:HIS65 3.3 12.2 0.1
CG A:HIS65 3.3 12.0 0.1
OE2 A:GLU62 3.4 17.2 1.0
OE1 A:GLU27 3.4 13.6 1.0
CB A:HIS65 3.6 11.8 0.1
CB A:HIS65 3.6 11.4 0.9
OE1 A:GLN141 4.1 20.5 1.0
O A:HOH459 4.1 24.2 0.9
CG1 A:VAL110 4.2 17.0 1.0
CG A:GLU27 4.3 10.6 1.0
NE2 A:HIS65 4.3 14.1 0.9
CG A:GLU62 4.3 10.3 1.0
CD2 A:HIS65 4.4 13.2 0.9
NE2 A:HIS65 4.4 12.2 0.1
CD2 A:HIS65 4.5 12.1 0.1
CA A:GLU62 4.5 9.3 1.0
CB A:GLU27 4.6 9.5 1.0
CB A:GLU62 4.7 9.4 1.0
O A:HOH310 4.7 26.3 1.0
CA A:GLU27 4.8 8.4 1.0
OE1 A:GLU107 4.9 15.8 0.5

Magnesium binding site 2 out of 13 in 7o63

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Magnesium binding site 2 out of 13 in the High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:17.1
occ:0.50
 MG A:MG202 0.0 17.1 0.5
O A:HOH306 1.9 18.8 0.5
OE2 A:GLU140 2.0 16.8 0.5
O A:HOH420 2.0 23.0 0.5
O A:HOH301 2.0 13.3 0.5
O A:HOH310 2.1 26.3 1.0
OG A:SER144 2.1 13.7 0.7
O A:HOH334 2.1 20.5 0.5
O A:HOH420 2.2 28.1 0.5
CD A:GLU140 2.9 15.7 0.5
MG A:MG202 3.1 21.2 0.5
O A:HOH307 3.2 32.8 1.0
CB A:SER144 3.3 13.0 0.3
CB A:SER144 3.3 12.2 0.7
OE1 A:GLU140 3.3 16.9 0.5
OG A:SER144 3.6 13.7 0.3
OE1 A:GLU61 3.7 28.6 1.0
O A:HOH510 3.7 27.3 0.5
O A:HOH366 3.8 18.1 1.0
OE1 A:GLN58 4.0 21.2 1.0
O A:GLU140 4.2 12.1 1.0
OE2 A:GLU107 4.2 14.1 0.5
CG A:GLU140 4.3 15.3 0.5
OE1 A:GLU107 4.3 13.7 0.5
CE1 A:HIS65 4.4 13.6 0.9
CA A:SER144 4.4 11.3 0.7
CA A:SER144 4.4 12.5 0.3
O A:HOH473 4.5 30.5 1.0
O A:HOH518 4.6 23.8 0.7
O A:HOH578 4.6 38.9 1.0
CD A:GLU107 4.6 13.1 0.5
O A:HOH439 4.7 22.5 0.5
OE1 A:GLU140 4.7 20.5 0.5
CD A:GLU61 4.8 24.4 1.0
NE2 A:HIS65 4.8 14.1 0.9
OE2 A:GLU62 4.9 17.2 1.0
N A:SER144 4.9 9.9 1.0
C A:GLU140 4.9 11.1 1.0
O A:HOH379 5.0 21.2 1.0

Magnesium binding site 3 out of 13 in 7o63

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Magnesium binding site 3 out of 13 in the High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:21.2
occ:0.50
 MG A:MG202 0.0 21.2 0.5
O A:HOH420 1.7 28.1 0.5
O A:HOH439 1.8 22.5 0.5
O A:HOH420 1.8 23.0 0.5
OE1 A:GLN58 2.1 21.2 1.0
OE1 A:GLU61 2.2 28.6 1.0
O A:HOH301 2.2 13.3 0.5
O A:HOH510 2.3 27.3 0.5
O A:HOH306 3.0 18.8 0.5
CD A:GLN58 3.0 16.7 1.0
MG A:MG202 3.1 17.1 0.5
O A:HOH334 3.1 20.5 0.5
CD A:GLU61 3.2 24.4 1.0
NE2 A:GLN58 3.2 24.8 1.0
OE2 A:GLU61 3.5 32.8 1.0
O A:HOH337 3.6 34.6 1.0
O A:HOH366 4.1 18.1 1.0
O A:HOH518 4.1 23.8 0.7
OE2 A:GLU140 4.2 16.8 0.5
OG A:SER144 4.3 13.7 0.7
O A:HOH578 4.3 38.9 1.0
O A:HOH307 4.4 32.8 1.0
O A:HOH518 4.4 20.6 0.3
CG A:GLN58 4.4 13.4 1.0
CG A:GLU61 4.5 14.6 1.0
CD2 A:HIS57 4.7 22.5 1.0
CA A:GLN58 4.9 9.5 1.0
CB A:GLU61 4.9 11.3 1.0
OE1 A:GLU147 4.9 17.5 1.0
CB A:GLN58 5.0 10.8 1.0

Magnesium binding site 4 out of 13 in 7o63

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Magnesium binding site 4 out of 13 in the High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:19.8
occ:0.50
 O A:HOH380 2.0 35.7 1.0
O A:HOH451 2.0 27.0 1.0
O A:THR135 4.1 18.7 1.0
O A:HOH486 4.2 22.2 0.5
O A:HOH664 4.5 32.6 0.5
O A:GLU134 4.6 12.7 0.6
CA A:THR135 4.6 14.5 1.0
O A:GLU134 4.8 11.5 0.4
O A:HOH486 4.8 21.2 0.5
C A:THR135 4.9 14.8 1.0
O A:HOH545 4.9 34.9 1.0
O A:HOH624 5.0 24.5 0.2
O A:HOH517 5.0 13.5 1.0

Magnesium binding site 5 out of 13 in 7o63

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Magnesium binding site 5 out of 13 in the High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:21.4
occ:0.40
 O A:HOH667 2.0 28.2 0.4
O A:HOH550 2.0 25.7 0.5
O A:HOH668 2.1 29.2 0.4
O A:HOH556 2.2 16.5 0.4
O A:HOH505 2.3 30.9 1.0
O A:HOH556 3.3 14.6 0.6
NH2 A:ARG7 4.1 19.5 0.4
O A:HOH639 4.1 30.2 0.5
NH2 A:ARG7 4.2 18.7 0.6
NE A:ARG7 4.2 17.4 0.6
NE A:ARG7 4.3 18.6 0.4
O A:HOH588 4.5 31.9 1.0
CZ A:ARG7 4.7 18.7 0.4
CZ A:ARG7 4.7 17.6 0.6

Magnesium binding site 6 out of 13 in 7o63

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Magnesium binding site 6 out of 13 in the High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:17.1
occ:0.50
 O A:HOH436 1.6 14.5 0.5
O A:HOH436 2.0 15.0 0.5
O A:HOH583 2.0 19.3 0.5
O A:HOH599 2.0 23.7 0.7
O A:HOH671 2.1 25.5 0.5
O A:HOH666 2.2 30.5 0.5
O A:HOH599 2.3 20.4 0.3
O A:HOH419 2.3 16.4 1.0
OD1 A:ASN25 4.3 9.1 1.0
O A:HOH565 4.3 29.2 0.5
O A:HOH656 4.3 26.1 1.0
O A:ARG22 4.3 8.7 1.0
O A:HOH655 4.3 51.9 1.0
O A:HOH593 4.3 23.6 1.0
O A:HOH630 4.4 18.4 1.0
O A:HOH674 4.5 46.4 1.0
O A:HOH412 4.6 24.5 1.0
O A:HOH562 4.8 30.8 0.5
CB A:LEU26 4.9 9.0 1.0
CB A:ARG22 5.0 9.7 0.5

Magnesium binding site 7 out of 13 in 7o63

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Magnesium binding site 7 out of 13 in the High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:20.3
occ:0.50
 OD1 A:ASN49 1.9 13.5 0.3
O A:HOH408 1.9 17.5 0.5
O A:HOH558 2.0 22.3 0.5
O A:HOH440 2.0 16.7 0.5
O A:HOH409 2.1 28.4 1.0
CG A:ASN49 2.9 12.8 0.3
ND2 A:ASN49 3.4 13.2 0.3
O A:HOH663 3.5 78.3 1.0
OG A:SER42 3.9 11.2 0.4
O A:HOH596 3.9 28.5 1.0
OD1 A:ASN49 4.1 16.4 0.7
OG A:SER52 4.2 10.7 1.0
CB A:ASN49 4.2 12.1 0.3
CB A:ASN49 4.3 13.0 0.7
O A:ASN49 4.4 9.4 1.0
CG A:ASN49 4.4 15.6 0.7
CB A:SER52 4.5 9.2 1.0
CA A:ASN49 4.6 11.5 0.3
CA A:ASN49 4.6 11.2 0.7
CG A:ARG53 4.7 13.6 0.5
O A:HOH474 4.8 25.5 1.0
CB A:SER42 4.8 10.6 0.6

Magnesium binding site 8 out of 13 in 7o63

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Magnesium binding site 8 out of 13 in the High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:11.7
occ:0.50
 O A:HOH626 2.0 12.9 0.5
O A:HOH600 2.1 15.0 1.0
O A:HOH385 4.2 12.5 1.0
CD A:LYS86 4.5 11.8 0.5
NZ A:LYS86 4.5 11.5 0.5
O A:HOH654 4.5 13.4 1.0
O A:HOH605 4.6 17.2 0.6
CE A:LYS87 4.6 13.6 0.6
CE A:LYS87 4.6 12.3 0.4
CE A:LYS86 4.7 12.8 0.5
CD A:LYS86 5.0 11.0 0.5

Magnesium binding site 9 out of 13 in 7o63

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Magnesium binding site 9 out of 13 in the High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:23.6
occ:0.50
 O A:HOH416 1.9 30.6 1.0
O A:HOH669 2.0 33.2 0.5
O A:HOH665 2.1 29.1 0.5
O A:HOH449 2.1 27.0 0.5
O A:HOH601 2.2 24.7 0.5
O A:HOH361 4.1 17.4 1.0
O A:HOH433 4.4 16.6 1.0
OE2 A:GLU17 4.5 13.3 1.0
O A:HOH537 4.6 39.1 1.0
CB A:PRO14 4.7 13.2 1.0
O A:HOH612 4.7 49.2 1.0
NH2 A:ARG81 4.9 14.7 0.2
CG A:PRO14 4.9 15.5 1.0
O A:HOH428 4.9 34.6 1.0

Magnesium binding site 10 out of 13 in 7o63

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Magnesium binding site 10 out of 13 in the High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of High Resolution Crystal Structure of Human Mitochondrial Ferritin (Hmtf) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg209

b:20.9
occ:0.50
 O A:HOH411 2.1 22.7 0.5
O A:HOH617 2.1 24.8 0.5
O A:HOH377 2.2 22.8 1.0
O A:HOH485 4.1 17.3 1.0
O A:HOH414 4.2 11.1 1.0
OD1 A:ASP171 4.2 10.3 1.0
O A:HOH500 4.4 32.5 0.5
OG1 A:THR172 4.4 15.4 0.5
ND2 A:ASN50 4.6 16.4 1.0
O A:HOH542 4.7 51.5 1.0
CG2 A:THR172 4.7 16.0 0.5
O A:HOH312 4.8 42.7 1.0

Reference:

S.Ciambellotti, A.Pratesi, G.Tassone, P.Turano, S.Mangani, C.Pozzi. Iron Binding in the Ferroxidase Site of Human Mitochondrial Ferritin. Chemistry 2021.
ISSN: ISSN 0947-6539
PubMed: 34343376
DOI: 10.1002/CHEM.202102270
Page generated: Thu Oct 3 02:33:40 2024

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